Fig. Fragment size distribution for a representative sample. Left, distribution of the fragment size lengths; right, autocorrelation coefficient showing the expected periodicity.

Fig. Heatmap showing correlation matrix between peaks.

Fig. Distribution of the TSS. Plot showing the distance from TSS against the read density.

Fig. Chromatin feature analysis showing the peak distribution across the chromatin.

Fig. Occupancy heatmap for peaks corresponding to selected genes (read from file genesets_allgenes.csv)

Fig. Occupancy heatmap for peaks corresponding to top 30 differentially binding peaks from each contrast.

Fig. Volcano plots showing peak fold changes (x axis9 and p-values (y axis).

Fig. Volcano plots showing peak fold changes (x axis9 and p-values (y axis). Colors correspond to peaks associated with genes from the ISG gene set.

Figs. Panel plots. Please use the figures from the report.

Fig. Motif analysis. Please use the motifs from the report.

Fig. PCA Principal component analysis (components 1 and 2).

Fig. Evidence plot for cytoprotection (Reactome gene set REACTOME_REGULATION_OF_HMOX1_EXPRESSION_AND_ACTIVITY, ID M41831).

Fig. Cluster profiler results separate by up- and down-regulated gene sets. Contrast uni_DMSO_vs_naive_ID0, database GO, subcategory BP.

Fig. Cluster profiler results separate by up- and down-regulated gene sets. Contrast DMSO_inf_vs_uninf_ID1, database GO, subcategory BP.

Fig. Cluster profiler results separate by up- and down-regulated gene sets. Contrast JQ_uninf_vs_naive_ID2, database GO, subcategory BP.

Fig. Cluster profiler results separate by up- and down-regulated gene sets. Contrast JQ_inf_vs_uninf_ID3, database GO, subcategory BP.

Fig. Cluster profiler results separate by up- and down-regulated gene sets. Contrast interaction_ID4, database GO, subcategory BP.

Fig. Cluster profiler results separate by up- and down-regulated gene sets. Contrast JQ_uninf_vs_DMSO_uninf_ID5, database GO, subcategory BP.

Fig. Cluster profiler results separate by up- and down-regulated gene sets. Contrast JQ_inf_vs_DMSO_inf_ID6, database GO, subcategory BP.

Fig. Cluster profiler results, alternate visualization

Fig. Distribution of higly occupied fragments (average number of reads > 100) by sample group.

Fig. Distribution of highly occupied fragments (average number of reads > 100) by sample group.

Table. Distribution of highly occupied fragments (average number of reads > 100) by sample group. Values are percentages of peaks assigned to the given region.

Feature DMSO infected DMSO uninfected JQ-1 infected JQ-1 uninfected naive uninfected
3’ UTR 0.53 0.44 0.53 0.55 0.56
5’ UTR 0.06 0.08 0.06 0.06 0.09
Distal Intergenic 13.34 13.01 18.54 17.67 13.95
Downstream 0.65 0.62 0.80 0.78 0.54
Exon 0.61 0.50 0.70 0.73 0.58
Intron 12.22 11.36 18.05 16.80 12.65
Promoter (1-2kb) 4.29 3.76 4.67 4.80 3.91
Promoter (2-3kb) 3.12 2.81 3.40 3.46 3.00
Promoter (<=1kb) 65.18 67.43 53.25 55.15 64.73

Table. Number of peaks significant at FDR < 0.05 in each contrast.

Contrast Up Down Total
uni_DMSO_vs_naive_ID0 0 0 0
DMSO_inf_vs_uninf_ID1 128 2 130
JQ_uninf_vs_naive_ID2 11003 4606 15609
JQ_inf_vs_uninf_ID3 5064 2092 7156
interaction_ID4 796 539 1335
JQ_uninf_vs_DMSO_uninf_ID5 7679 3755 11434
JQ_inf_vs_DMSO_inf_ID6 17137 8169 25306